// get_arg.h
//

#if !defined(GETARG_H)
#define GETARG_H

#include <string>
//#include <iosfwd>
#include <sstream>
#include <iostream>
#include <fstream>
#include <vector>

#include <program_options_helper.h>

class t_program_args : public program_options_helper::t_std_program_args_with_errors
{
	friend
	bool process_command_line_options(int argc, char* argv[], t_program_args& args);
public:
	std::string				file_seq;
	std::string				regex ;
	bool					cdna;
	bool					wrap;
	bool					kaks;
	std::string				name1 ;
	std::string				name2 ;
	std::vector<unsigned>	pair_indices;
	std::string				comment_letters;


};

bool process_command_line_options(int argc, char* argv[], t_program_args& args);
#endif //GETARG_H
